News:Eukaryotic Metabarcoding workshop

Question

[carlopecoraro2]

Dear all

we still have a few places available on our next Eukaryotic-metabarcoding workshop: http://www.physalia-courses.org/courses/course4/

This course is being delivered by Dr. Owen S. Wangensteen, an expert in the application of molecular techniques to the study of marine ecological issues and biodiversity assessment of marine benthic ecosystems, including high-throughput sequencing and bioinformatics. He is currently working at the University of Salford (UK), actively participating on the development of new metabarcoding techniques for the assessment of biodiversity in the marine realm (both in benthic and seawater samples), as a member of Project SeaDNA (NERC, UK).

The course will run from Monday 20th to Friday 24th February 2017 in Berlin, Germany.

Overview:

Metabarcoding techniques are a set of novel genetic tools for qualitatively and quantitatively assessing biodiversity of natural communities. Their potential applications include (but are not limited to) accurate water quality, soil diversity assessment, trophic analyses of digestive contents, diagnosis of health status of fisheries, early detection of non-indigenous species, studies of global ecological patterns and biomonitoring of anthropogenic impacts. This workshop gives an overview of metabarcoding procedures with an emphasis on practical problem-solving and hands-on work using analysis pipelines on real datasets. After completing the workshop, students should be in a position to (1) understand the potential and capabilities of metabarcoding, (2) run complete analyses of metabarcoding pipelines and obtain diversity inventories and ecologically interpretable data from raw next-generation sequence data and (3) design their own metabarcoding projects, using bespoke primer sets and custom reference databases. All course materials (including copies of presentations, practical exercises, data files, and example scripts prepared by the instructing team) will be provided electronically to participants.

Intended audience:

This workshop is mainly aimed at researchers and technical workers with a background in ecology, biodiversity or community biology who want to use molecular tools for biodiversity research and at researchers in other areas of bioinformatics who want to learn ecological applications for biodiversity-assessment. In general, it is suitable for every researcher who wants to join the growing community of metabarcoders worldwide. This workshop will review mostly techniques and software useful for eukaryotic metabarcoding. Another workshop focused on procedures currently used in microbial metabarcoding will be available from Physalia-courses.

Teaching format:

The workshop is delivered over ten half-day sessions (see the detailed curriculum below). Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organizer’s discretion.

Assumed background:

No programming or scripting experience is necessary, but some previous expertise using the Linux console and/or R will be most welcome. All examples will be run in a Linux environment. Thus, either a Linux PC or a virtual box running Linux under Windows or Mac environment will be needed. MacOSX systems might be OK, although installation of some additional Python packages might be needed in that case. The syllabus has been planned for people which have some previous experience running simple commands in Linux and using the R environment (preferently RStudio) for performing basic plots and statistical procedures. You will need to have a laptop with Python 2.7 installed for running OBITools, the main metabarcoding software package we will be using during the course, but no experience with Python is necessary. If in doubt, take a look at the detailed session content below or contact Dr. Owen S. Wangensteen ([e-mail]).

Course programme:

Monday 20th – Classes from 09:30 to 17:

• Session 1. Introduction to metabarcoding procedures. The metabarcoding pipeline.
• Session 2. Metabarcoding markers. Primer design. PCR and library preparation protocols.

Tuesday 21st – Classes from 09:30 to 17:

• Session 3. The OBITools pipeline. First steps and quality control.
• Session 4. Clustering algorithms. Fixed and variable identity thresholds.

Wednesday 22nd – Classes from 09:30 to 17:

• Session 5. Taxonomic assignment. The ecotag algorithm. Reference databases.
• Session 6. Generating, improving and curating reference databases.

Thursday 23rd – Classes from 09:30 to 17:30

• Session 7. Refining the final dataset. Collapsing, renormalizing and blank correction.
• Session 8. Analysing the final dataset. α- and ß- diversity patterns.

Friday 24th – Classes from 09:30 to 17:30

• Session 9. Presenting the final results. Online resources and future developments. -Session 10. Optional free afternoon to cover previous modules and discuss data.

Application deadline is the 20th of January 2017.

--
Carlo Pecoraro, Ph.D
Physalia-courses Coordinator
[e-mail]
http://www.physalia-courses.org/
Twitter: @physacourses
mobile: [phone]
Skype: carlo_pecoraro

Answer 1

[carlopecoraro2]

We have the last two places available (first-come, first-served) for the Workshop on " Eukaryotic-Metabarcoding": http://www.physalia-courses.org/courses/course4/

Answer 2

[carlopecoraro2]

The full-text of Owen's paper on deep-sea metabarcoding is, at last, in PeerJ: https://peerj.com/articles/2807/

Answer 3

[carlopecoraro2]

New Venue: our course on "Eukaryotic-Metabarcoding" will run from 20th - 24th February 2017 at the Freie Universität Berlin, Institute of Biology, Königin-Luise-Str. 1-3, 14195 Berlin-Dahlem!